Validation of tools to accelerate high-speed CFD simulations using OpenFOAM

Local time stepping (LTS) and adaptive mesh refinement (AMR) have been implemented into rhoCentralFoam, a compressible solver within the open source computational fluid dynamics (CFD) code OpenFOAM. The LTS solver has been validated using a compressible Couette channel with heat transfer and a supersonic at plate. An excellent concurrence is found for these cases in comparison with the solutions with the obtained results being, respectively, 2.56 and 8.96 times faster compared to the unmodified solver. The AMR solver was employed to simulate hypersonic flow over a 30° wedge, and the Sod shock tube test case, and has also achieved satisfactory agreement with the analytical solutions. These results highlight the potentially significant computational cost savings that may be achieved when solving high-speed, compressible flows using this approach

Comparison of Intrusive and Non-Intrusive Methods for Corrosion Monitoring of Fuel Processing Systems

This presentation contains an assessment of the best overall corrosion monitoring device, intrusive or non-intrusive, for use in the petrochemical industry. Corrosion in the petrochemical industry is a large issue because it causes a deterioration of pipe integrity in fuel processing systems. A reduction of pipe wall integrity due to corrosion could result in a leak or an explosion of fuel processing lines since those systems function at high pressures. The use of corrosion monitoring systems in the petrochemical industry helps to detect early signs of corrosion prior to failure so that proper maintenance can be performed to prevent catastrophe. To simulate those types of systems a test cell was designed to adequately fit two corrosion monitoring devices. Each device determines corrosion rate by measuring pipe wall thickness over time using ultrasonic technology or by measuring resistance across a degrading reference element. The corrosive medium used to corrode the inside of the test cell is glacial acetic acid (\u3e99.7% purity). Measurements of pipe wall thickness were taken before and after testing and are used as a reference point to compare against each device’s measurement. Relative accuracy, response time, safety, and reliability are used as criteria for determining the best monitoring device. Overall, the Microcor ER probe proved to be the better of the two devices as determined by the criteria listed above and the time allowed for testing

An open-source hybrid CFD-DSMC solver for high speed flows

During re-entry, a spacecraft will experience flow conditions ranging from highly rarefied to continuum. To simulate regions in between, a hydrodynamic-molecular gas hybrid solver should be used to provide accuracy and effciency. Currently available hybrid codes are in-house codes or do not provide the capabilities to simulate all of the phenomena a spacecraft will experience during re-entry. An open-source CFD-DSMC hybrid code is being developed within the OpenFOAM framework, coupling the solvers dsmcFoam and hy2Foam. In this paper, comparison between the CFD, DSMC and hybrid codes have been performed for simple cases. The dsmcFoam and the hybrid code have shown to compare satisfactorily

Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range

Background Approximately 50% of freshwater turtles worldwide are currently threatened by habitat loss, rural development and altered stream flows. Paradoxically, reptiles are understudied organisms, with many species lacking basic geographic distribution and abundance data. The iconic Irwin’s turtle, Elseya irwini, belongs to a unique group of Australian endemic freshwater turtles capable of cloacal respiration. Water resource development, increased presence of saltwater crocodiles and its cryptic behaviour, have made sampling for Irwin’s turtle in parts of its range problematic, resulting in no confirmed detections across much of its known range for > 25 years. Here, we used environmental DNA (eDNA) analysis for E. irwini detection along its historical and contemporary distribution in the Burdekin, Bowen and Broken River catchments and tributaries. Five replicate water samples were collected at 37 sites across those three river catchments. Environmental DNA was extracted using a glycogen-aided precipitation method and screened for the presence of E. irwini through an eDNA assay targeting a 127 base pair-long fragment of the NADH dehydrogenase 4 (ND4) mitochondrial gene. Results Elseya irwini eDNA was detected at sites within its historic distribution in the lower Burdekin River, where the species had not been formally recorded for > 25 years, indicating the species still inhabits the lower Burdekin area. We also found higher levels of E. iriwni eDNA within its contemporary distribution in the Bowen and Broken Rivers, matching the prevailing scientific view that these areas host larger populations of E. irwini. Conclusions This study constitutes the first scientific evidence of E. irwini presence in the lower Burdekin since the original type specimens were collected as part of its formal description, shortly after the construction of the Burdekin Falls Dam. From the higher percentage of positive detections in the upper reaches of the Broken River (Urannah Creek), we conclude that this area constitutes the core habitat area for the species. Our field protocol comprises a user-friendly, time-effective sampling method. Finally, due to safety risks associated with traditional turtle sampling methods in the Burdekin River (e.g., estuarine crocodiles) we propose eDNA sampling as the most pragmatic detection method available for E. irwini

A two-temperature open-source CFD model for hypersonic reacting flows, part two : multi-dimensional analysis

hy2Foam is a newly-coded open-source two-temperature computational fluid dynamics (CFD) solver that has previously been validated for zero-dimensional test cases. It aims at (1) giving open-source access to a state-of-the-art hypersonic CFD solver to students and researchers; and (2) providing a foundation for a future hybrid CFD-DSMC (direct simulation Monte Carlo) code within the OpenFOAM framework. This paper focuses on the multi-dimensional verification of hy2Foam and firstly describes the different models implemented. In conjunction with employing the coupled vibration-dissociation-vibration (CVDV) chemistry–vibration model, novel use is made of the quantum-kinetic (QK) rates in a CFD solver. hy2Foam has been shown to produce results in good agreement with previously published data for a Mach 11 nitrogen flow over a blunted cone and with the dsmcFoam code for a Mach 20 cylinder flow for a binary reacting mixture. This latter case scenario provides a useful basis for other codes to compare against

Marine Dendryphiella-Spezies aus verschiedenen geographischen Lagen: ein integriertes, polyphasisches Verfahren zu ihrer Taxonomie und Physioökologie

The marine Dendryphiella species, D. arenaria and D. salina, were studied to determine their taxonomic and phylogenetic position as well as their genetic and phenotypic differences. Strains were isolated from various substrates in subtropical and temperate waters. Genomic DNA was extracted from strains of Dendryphiella and Scolecobasidium species and their gene sequences analyzed. Production of enzymes using cultural methods and API ZYM assay, as well as BIOLOG Phenotype MicroArrays were used to assess the ability of the Dendryphiella strains to utilize different substrata. Secondary metabolic profiles of their crude culture extracts were also detected by TLC and HPLC-DAD. Physiological responses to abiotic and biotic factors as well as their antimicrobial activities were also studied on the different D. arenaria and D. salina strains. Sequence analysis of the ITS 1 and 2, tef1 and rpb2 genes showed that the marine Dendryphiella strains formed two sister clades, which correspond to D. arenaria and D. salina. Both species belong to the family Pleosporaceae, with Pleospora spp. (anamorph Stemphylium spp.) as the next taxonomic relative. All Scolecobasidium species sequenced formed a distinct genetically isolated phylogenetic group outside of the class Loculoascomycetes, and thus, are not genetically related to Dendryphiella. The Dendryphiella species from different geographical locations exhibited similar enzyme and secondary metabolic profiles, but differed significantly in their carbon utilization profiles which can be used to discriminate not only the two species, but also sub-populations of D. arenaria and D. salina. All tested strains grew on the different investigated parameters demonstrating phenotypic plasticity, but optimally on culture medium with added marine salts, at pH values between 6.5 – 8.0 and at an incubation temperature of 25 oC. The culture extracts were antimicrobial, though production of the biologically active metabolites was strain specific.Die marinen Dendryphiella-Spezies D. arenaria und D. salina wurden untersucht, um ihre Taxonomie und Phylogenie so wie ihre genetischen und phänotypischen Unterschiede zu klären. Die Stämme wurden von subtropischen und gemäßigten Küstengebieten isoliert. Aus der genomischen DNA von Dendryphiella und Scolecobasidium - Spezies wurden Gene analysiert. Die Untersuchung von Enzymproduktion und Substratverwertung der Dendryphiella-Stämme erfolgte mit konventionellen Kultivierungsmethoden, API ZYM Assay sowie BIOLOG Phenotype MicroArrays. Die Profile der Sekundärmetabolite aus Kulturrohextrakten wurden mittels TLC und HPLC-DAD bestimmt. Verschiedene D. arenaria- und D. salina -Stämme wurden auf ihre physiologische Antwort auf die biotischen und abiotischen Faktoren sowie auf antimikrobielle Aktivitäten hin untersucht. Die Sequenzanalyse der ITS 1 und 2, tef1 und rpb2-Gene ergab, dass die marinen Dendryphiella – Stämme zwei Gruppen bilden, die zu D. salina und D. arenaria gehören. Sie gehören zur Familie der Pleosporaceae mit naher Verwandtschaft zu der Gattung Pleospora (Anamorph – Stemphylium spp). Alle sequenzierten Scolecobasidium–Spezies bilden eine phylogenetische Gruppe außerhalb der Loculoascomycetes-Klasse. Es besteht keine genetische Verwandtschaft zu Dendryphiella-Spezies. Die beiden Dendryphiella-Arten zeigen ähnliche Enzym- und Metabolitprofile. Sie unterscheiden sich jedoch signifikant in der Substratverwertung, was eine Differenzierung nicht nur der beiden untersuchten Spezies, sondern auch von geographischen Subpopulationen von D. arenaria und D. salina ermöglicht. Das Wachstum der Stämme unter den diversen Bedingungen weist auf ihre phänotypische Plastizität hin. Als optimal erweisen sich für die Pilzisolate ein Kulturmedium mit Meersalz, ein pH-Wert zwischen 6.5 – 8,0 sowie eine Temperatur von 25 °C. Die Kulturextrakte zeigen antimikrobielle Eigenschaften; die Produktion von biologisch aktiven Metaboliten ist jedoch stammspezifisch

Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA, and actin filaments

We used fluorescence spectroscopy and EM to determine how binding of ATP, nucleation-promoting factors, actin monomers, and actin filaments changes the conformation of Arp2/3 complex during the process that nucleates an actin filament branch. We mutated subunits of Schizosaccharomyces pombe Arp2/3 complex for labeling with fluorescent dyes at either the C termini of Arp2 and Arp3 or ArpC1 and ArpC3. We measured Förster resonance energy transfer (FRET) efficiency (ET_(eff)) between the dyes in the presence of the various ligands. We also computed class averages from electron micrographs of negatively stained specimens. ATP binding made small conformational changes of the nucleotide-binding cleft of the Arp2 subunit. WASp-VCA, WASp-CA, and WASp-actin-VCA changed the ET_(eff) between the dyes on the Arp2 and Arp3 subunits much more than between dyes on ArpC1 and ArpC3. Ensemble FRET detected an additional structural change that brought ArpC1 and ArpC3 closer together when Arp2/3 complex bound actin filaments. VCA binding to Arp2/3 complex causes a conformational change that favors binding to the side of an actin filament, which allows further changes required to nucleate a daughter filament

Atomic-Level Mechanisms for Phospholamban Regulation of the Calcium Pump

AbstractWe performed protein pKa calculations and molecular dynamics (MD) simulations of the calcium pump (sarcoplasmic reticulum Ca2+-ATPase (SERCA)) in complex with phospholamban (PLB). X-ray crystallography studies have suggested that PLB locks SERCA in a low-Ca2+-affinity E2 state that is incompatible with metal-ion binding, thereby blocking the conversion toward a high-Ca2+-affinity E1 state. Estimation of pKa values of the acidic residues in the transport sites indicates that at normal intracellular pH (7.1–7.2), PLB-bound SERCA populates an E1 state that is deprotonated at residues E309 and D800 yet protonated at residue E771. We performed three independent microsecond-long MD simulations to evaluate the structural dynamics of SERCA-PLB in a solution containing 100 mM K+ and 3 mM Mg2+. Principal component analysis showed that PLB-bound SERCA lies exclusively along the structural ensemble of the E1 state. We found that the transport sites of PLB-bound SERCA are completely exposed to the cytosol and that K+ ions bind transiently (≤5 ns) and nonspecifically (nine different positions) to the two transport sites, with a total occupancy time of K+ in the transport sites of 80%. We propose that PLB binding to SERCA populates a novel (to our knowledge) E1 intermediate, E1⋅H+771. This intermediate serves as a kinetic trap that controls headpiece dynamics and depresses the structural transitions necessary for Ca2+-dependent activation of SERCA. We conclude that PLB-mediated regulation of SERCA activity in the heart results from biochemical and structural transitions that occur primarily in the E1 state of the pump